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Series GSE68204 Query DataSets for GSE68204
Status Public on Apr 22, 2016
Title Gene and microRNA expression predictive of tumour response in patients treated with pCRT for LARC
Organism Homo sapiens
Experiment type Expression profiling by array
Non-coding RNA profiling by array
Summary The goal of this work is to find robust predictors of tumor response to preoperative chemoradiotherapy in LARC patients.
Preoperative chemoradiotherapy (pCRT) followed by surgery is the standard treatment for locally advanced rectal cancer (LARC). However, tumour response to pCRT is not uniform and there are no effective predictive methods. This study investigated whether specific gene and miRNA expression is associated with response to pCRT. Tissue biopsies were obtained from patients before pCRT and resection. Gene and miRNA expression was analyzed using one-color microarrays technique comparing signatures between responders (R) and not responders(NR), as measured by tumour regression grade (TRG). Two groups composed by 38 “exploration cohort” and 21 “validation cohort” LARC patients respectively were considered, for a total of 32 NR and 27 R patients. In the first cohort, SAM Two Class identified 256 genes and 29 miRNAs differentially expressed between NR and R. The anti-correlation analysis showed that the same 8 miRNA interacted with different networks of transcripts. The miR-630 appeared only with NR patients and was anti-correlated with a single transcript: RAB5B. After PAM, resulted as strong predictors of tumour responsen the following 8 transcripts: TMEM188, ITGA2, NRG, TRAM1, BCL2L13, MYO1B, KLF7 and GTSE1. Using this gene set, an unsupervised cluster analysis applied to the second cohort assigned the patients to the NR or R group with 85.7% accuracy with a sensitivity of 90% and a specificity of 82%. All the three parametres reached 100% when the two cohorts were considered together.
 
Overall design Tissue biopsies were obtained from patients before pCRT and resection. Two groups composed by 38 and 21 LARC patients respectively were considered, for a total of 32 NR and 27 R patients both for gene and miRNA expression experiments
 
Contributor(s) Millino C, Pacchioni B
Citation(s) 27225591
Submission date Apr 23, 2015
Last update date Jan 23, 2019
Contact name Gerolamo Lanfranchi
E-mail(s) [email protected]
Phone +39-0498276219
Organization name University of Padova
Department CRIBI - Biotechnology Center and Biology Department
Lab Functional Genomics Lab
Street address Via U. Bassi, 58/B
City Padova
ZIP/Postal code 35131
Country Italy
 
Platforms (2)
GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
GPL10850 Agilent-021827 Human miRNA Microarray (V3) (miRBase release 12.0 miRNA ID version)
Samples (125)
GSM1665617 TumorRectalBiopsy_ResponderpCRT82e_GErep1
GSM1665618 NormalRectalBiopsy_ResponderpCRT82e_GErep1
GSM1665619 TumorRectalBiopsy_NonResponderpCRT91_GErep1
Relations
BioProject PRJNA282020

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE68204_Normalized_signal_exploration_cohort.txt.gz 7.4 Mb (ftp)(http) TXT
GSE68204_Normalized_signal_validation_cohort.txt.gz 4.1 Mb (ftp)(http) TXT
GSE68204_RAW.tar 632.2 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data are available on Series record
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